The arrogant, narcissistic Andrew Wakefield is going to bring a lawsuit against Brian Deer, the dogged Times of London reporter who not only uncovered that the original Lancet article authored by Wakefield was filled with errors, but uncovered fraud committed by Wakefield.

Recently, I discussed how science works. It’s not a belief. It’s not a random set of rules. It is a rational and logical process to determine cause and effect in the natural world. Pseudoscience, by its very nature, ignores the scientific process; instead, it claims to come to conclusions through science, usually by using scientific sounding words, but actually avoids the scientific process. They tend to use logical fallacies to make their case. Just to be clear, logical fallacy is essentially an error of reasoning. When a pseudoscientist makes a claim, or attempts to persuade the public of this claim, and it is based on a bad piece of reasoning, they commit a fallacy.

There are several types of logical fallacies that they employ. My favorites are Appeals to Antiquity, or old ideas are somehow better than new ideas; Appeals to Authority, or someone who should know better supports the claim even if everyone else does not; Appeals to Popularity, or everyone does it, so it must be useful; and the Genetic Fallacy, where the source is more matter than the merits of the evidence. Logical fallacies are so prevalent in skeptical community, there are websites devoted to describing them.

So how can you tell the difference between science and pseudoscience in medicine? In medicine, we gather and analyze evidence in one of two ways.

Almost any medical product, device, drug or procedure must, by law, must studied in a Randomized Controlled Trial, which is sometimes called a clinical trial. Essentially, it is a scientific experiment, designed to test the hypothesis of whether the safety and efficacy of a particular medical product is better than a placebo. That is, does the medical product produce results better than doing nothing at all. This is the “gold standard” of investigation, and if the study does confirm the hypothesis, you can be assured it has a benefit to your life (although the degree may be subject to argument). Alternative medicine just doesn’t do this (most of their reasoning is that their beliefs just doesn’t fit into the clinical trial model), so their is no proof that their products work. A clinical trial usually has thousands of participants, and is done in a manner that the patient and the physician do not know who is and who is not receiving the treatment. The results are analyzed statistically and published in peer-reviewed journals. Furthermore, the results are reviewed and investigated by the FDA (and legal bodies in other countries), before a drug or device can be used by a physician. This is an expensive and time-consuming process, in which alternative medicine hardly ever participates.

Now it’s not ethical to test every medical hypothesis with a clinical trial. For example, we know that smoking is bad for your health. Yet, tobacco manufacturers love to insist that there has never been a clinical trial that makes this conclusion. The reason that is true is that it would be unethical to give one group of adults cigarettes for 20 years and another group nothing to see if one would die at a higher rate. So we use epidemiological studies to determine if we can see in a population whether a cause has an effect. We can review records of thousands of smokers to see what the effect will be. Once again, pushers of alternative medicine therapies have not published a study of all the patients who might have used their therapy and see the result. Epidemiology is a scientific process that is critical to preventative medicine–without it, we cannot know if some behavior or public health issue has a causal effect on health.

Remember, anecdotes (“my mother’s friend’s cousin’s daughter was cured by eating this leaf”) are not reasons to accept alternative medicine. Even anecdotes that try to sound like science (“90 out of 100 people think this leaf does work”) aren’t a reason to “believe” in a pseudoscience.

You might have heard that taking lots of Vitamin C helps prevent colds. It doesn’t. And that conclusions is supported by large clinical trials, so unless you are afflicted by scurvy, there’s no reason to take large doses of the vitamin. And that’s the difference between real science and pseudoscience.

Peter Duesberg is an AIDS denialist. I don’t mind scientists that try to press for a new theory. It happens more often than one would think, but right now, the evidence that HIV causes AIDS is overwhelming. He’s like the creationist of the virology world..

He refutes the effectiveness of anti-retroviral drugs, without providing much evidence, but using this refutation as his “evidence”.

His rebuttal of the clear cut data of the disaster in South Africa when the government accept the AIDS denialism and anti-retrovirals usage dropped has been refuted a number of times.

Note that other journals turned him down. The Italian Journal of Anatomy and Embryology is what is a called a “low impact journal.” It means that the quality of the journal and its readership numbers are quite a bit lower than higher level journals.

I decided to write a three-part article here that partially describes how they make their case, not necessarily why humans accept it so easily. I’m not a psychiatrist, and I certainly don’t play one on TV. I thought we should start with the scientific method, or how real science works.

I always get suspicious when someone makes an argument with the statement of “it’s been proven to work”, “the link is proven”, or, alternatively, they state some negative about scientifically supported therapies. Typically, I hear these kinds of statements from the pseudoscience pushing crowd. For example, real science has debunked the “there is a proven link between vaccines and autism,” a common and popular pseudoscientific belief. Or that most alternative medicine (CAM) therapies work based on numerous logical fallacies that suspends reason, and accepts “belief” in the therapy, something that evidence-based medicine just doesn’t do.

In fact, science rarely uses the term “proven”, because the scientific method is not a system to make a definitive answer on any question–scientists always leave open the possibility of an alternative hypothesis that can be tested. If the alternate hypothesis can be supported through experimentation, then it can replace the original one. When an alternative medicine or junk science supporter states “it has been proven,” ask where is the evidence. What is more troubling is that someone who believes in these therapies cannot imagine that they don’t work, what is called falsification, which is a hallmark of good science. Whenever I hear that a scientist say, “we were wrong, it doesn’t work,” my retort is “excellent, good science.”

The scientific method is an unbiased systematic approach to answer questions about the natural world, including medicine. It has several basic steps:

Define the question–this could be anything from “does this compound have an effect on this disease?” or “how does this disease progress?”

Observations–this is the subjective part of science. Do we observe trends or anomalies? Does a physician notice that every patient from a town or neighborhood exhibit the same disease? A lot of science arises from observations of the natural world. One of the most famous stories in the early history of medicine is when Edward Jenner observed that milkmaids rarely were infected by smallpox because they were exposed to cowpox, a less virulent disease.

Hypothesis–taking the observations, create a hypothesis that can be tested. In Jenner’s case, he hypothesized that exposure to cowpox immunized individuals to small pox.

Experiment–simply, the scientist then tests the hypothesis with experiments and collect the data. The experiments are not designed to solely validate the hypothesis but may also attempt to contradict it.

Analyze–this requires statistics to determine the significance or results.

Interpret–sometimes the data leads to a revision of the hypothesis, which means the scientist has to return to steps 3-6. Or it confirms or supports the hypothesis, which means the researcher can move to Step 7.

Publish results–in today’s scientific community, the results require peer-review, which subjects the data, analysis and interpretation to the scrutiny of other scientists before publication. This is a critical step that ensures that the results can stand up to criticism. It does not prove anything, but it does support the hypothesis.

Retesting–Many times the research is repeated by others, or the hypothesis may be slightly revised with additional data. Science is not static, it constantly revises theories as more data is gathered. For this reason alone, science is not an absolute, it is constantly seeking new data.

Science is an evidence-based systematic analysis without inherent opinion or emotion. In other words, it is a method to cut through opinions and anecdotal observations, so that one can have some reasonable expectation that a medicine or device will work as planned. CAM fails to utilize scientific method. Supporters of CAM usually perform experiments to confirm the hypothesis, never to contradict it. It is the fundamental principle of falsifiability, that is, that if a hypothesis is false, it can be shown in experimentation that allows science to have an open mind about the world. When you speak to a believer of CAM, they almost never assume that their treatment cannot work.

It’s interesting that CAM and pseudoscience start out with observations of the real world. For example, CAM therapies sometimes work, not because of the therapies themselves, but because humans just get better from many diseases. So, these CAM therapies rely upon confirmation bias, that is, the tendency to accept information that supports your beliefs, or even post hoc ergo propter hoc, a logical fallacy which says “since that event followed this one, that event must have been caused by this one.” Humans too often conflate correlation and causation. Just because events follow one another, that doesn’t mean one causes the other. I suppose that’s how superstitions arise.

Part 2 of this discussion will be out as soon as I write it. It will discuss how to tell what is “proven” or what is science. Stay tuned.

Brian Deer, a reporter for the Sunday Times of London, wrote an article in the British Medical Journal that showed that Dr. Wakefield not only was in error, but probably altered key facts to show a link to autism, and outright fraudulent act. In the meantime, 10 of the 12 original co-authors of the Lancet article retracted their authorship. Then, in early 2010, the Lancet retracted the paper with this statement:

…it has become clear that several elements of the 1998 paper by Wakefield et al are incorrect, contrary to the findings of an earlier investigation. In particular, the claims in the original paper that children were “consecutively referred” and that investigations were “approved” by the local ethics committee have been proven to be false. Therefore we fully retract this paper from the published record.

Of course, a recent review of studies of the links between vaccines and autism find that there is no scientific support for the link. They concluded:

No credible evidence of an involvement of MMR with either autism or Crohn’s disease was found.

This might be an intellectual or philosophical discussion of science, except for one major problem. Vaccination rates have dropped in the UK, to as low as 85%. In 2006, there were 449 cases of measles in the UK. Before Wakefield’s report, there were only 56 cases in the UK in 1998. In the US, there have been measles and pertussis (whooping cough) outbreaks attributed to the falling vaccination rate (falling from 98% to 92% in a few years).

What worries me is what do we do when a scientist and professional like Andrew Wakefield publishes an article that sets the medical world on its figurative head? The great thing about science is that it is not dogmatic. Researchers moved quickly to understand the link, then to debunk it. And it was a trained journalist, who uncovered the fraud. But the consequences of that one article carries on today. People still think that vaccines cause everything. It doesn’t. Nevertheless, when it comes to medicine and science, we shouldn’t listen to Playboy Playmates.

Go get your children vaccinated. The risk from measles far outweighs the non-risk of autism.

Bad news, but there appears to be a few other vaccines in early testing. As an aside, whenever I read from the anti-vaccination crowd how vaccines aren’t tested, note that over 8,000 were tested in this trial.

Just a brief housekeeping note. Many of the links in this blog will point to an associated Wikipedia article. I, in fact, read and edit those articles, so I won’t make a link to an article that doesn’t make my point. It is supposed to be the epitome of a democratic encyclopedia, one that anyone can edit. It is free to read, and it has become the number one hit for almost any key subject, whether popular or obscure. Other than Obama’s own websites, the Wikipedia article about him is the first google hit.

I have mixed feelings about Wikipedia. There has been significant criticism of the project, which itself reduces the confidence in its quality and its usefulness. My concerns about these articles rest in a few key areas:

Quality of writing. Some of the writing is just plain bad. Some of it is a result of poor writing skills from English-speaking and non-English speaking contributors. But some of it is also from a waffling or trivial writing style. Worse yet, the prose is often not very engaging. Sometimes, it’s so difficult to read it, that one is apt to dismiss the article as being useless, even if it has useful knowledge.

Neutrality. Wikipedia has a vaunted policy called the Neutral Point of View, often abbreviated as NPOV. At its core, it states that an article should be written to represent all significant views that have been published by reliable sources. Two major problems arise from this policy. First, since it is very subjective, editors literally beat each other over the head with this policy. Second, and more importantly, NPOV drives articles to their worst. Academic articles usually state a point of view. You cannot read a book about the Holocaust without reading the point of view of the author. A medical article nearly always presents a point of view, albeit one supported by scientific research. Worse yet, editors will claim that a neutral article should include fringe theories. I edit medical and science articles anonymously, and I find myself either editing out strange, unscientific ramblings from these articles.

Vandalism. Because articles are almost always available to be edited by anyone, there is a certain level of vandalism that occurs, everything from “Joe was here” to profanity to much more subtle, insidious vandalism that is difficult to identify. More often than Wikipedia is willing to admit, this subtle vandalism remains in the article, often leading to inaccurate or incorrect information. This edit to the article on Martin Luther King, Jr remained for over 4 hours, despite the overt racism written into the article. There are numerous cases of these type of problems.

Lack of expertise. Because most editors are anonymous (a small subset of editors use their real names), it is nearly impossible to know the quality of edits from specific editors. I believe that smart people can write about anything. But, lacking an education in neurophysiology, how do I know if the article on dementia is of high or low quality? Whenever I read an article, I check the references. A high number of references means that usually the writing is supported by academic research. Wikipedia will need to fix this issue.

Anti-intellectualism. As a corollary to the lack of expertise is the pervasive contempt amongst Wikipedia editors against expert editors. There is a class of editors called “admins” who, more or less, act as the police, judge and jury for the project. They have the ability to pass summary judgement upon any editor. As a class, they are a part of the anti-intellectual core of the project. There are a few admins with expertise on science, historical, medical and other areas, but they generally keep a low profile.

So why do I link to Wikipedia articles? They may not be the best I can find on the internet, but these articles are, in general, fairly useful and provide an adequate background for a topic. When I find better sources for particular information, I use it.

I leave my readers with this warning about Wikipedia: read the articles with a critical eye as you do anything else you read. The problem is critical reading is not a skill I see very often these days.